Starting phenix.real_space_refine on Wed Sep 17 04:14:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g9x_51160/09_2025/9g9x_51160.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g9x_51160/09_2025/9g9x_51160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9g9x_51160/09_2025/9g9x_51160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g9x_51160/09_2025/9g9x_51160.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g9x_51160/09_2025/9g9x_51160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g9x_51160/09_2025/9g9x_51160.map" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 22 5.16 5 C 2630 2.51 5 N 622 2.21 5 O 678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3955 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1906 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 73 Unusual residues: {' K': 3, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Restraints were copied for chains: B Time building chain proxies: 1.39, per 1000 atoms: 0.35 Number of scatterers: 3955 At special positions: 0 Unit cell: (60.736, 70.72, 89.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 22 16.00 O 678 8.00 N 622 7.00 C 2630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 144.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 908 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 88.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 1 through 52 removed outlier: 4.237A pdb=" N ASN A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Proline residue: A 33 - end of helix removed outlier: 3.598A pdb=" N GLN A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 103 through 143 Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 155 through 182 removed outlier: 3.713A pdb=" N LEU A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 217 through 243 removed outlier: 3.539A pdb=" N THR A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 4.113A pdb=" N THR A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 Processing helix chain 'B' and resid 2 through 52 removed outlier: 5.601A pdb=" N GLU B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Proline residue: B 33 - end of helix removed outlier: 3.597A pdb=" N GLN B 46 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 143 Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 155 through 182 removed outlier: 3.712A pdb=" N LEU B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 243 removed outlier: 3.539A pdb=" N THR B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 248 removed outlier: 4.115A pdb=" N THR B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 252 314 hydrogen bonds defined for protein. 924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.56 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 612 1.32 - 1.44: 1146 1.44 - 1.56: 2262 1.56 - 1.68: 0 1.68 - 1.80: 34 Bond restraints: 4054 Sorted by residual: bond pdb=" CBC Y01 B 302 " pdb=" OAW Y01 B 302 " ideal model delta sigma weight residual 1.437 1.467 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" CBC Y01 A 302 " pdb=" OAW Y01 A 302 " ideal model delta sigma weight residual 1.437 1.467 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" CB ILE B 200 " pdb=" CG2 ILE B 200 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.60e+00 bond pdb=" CB ILE A 200 " pdb=" CG2 ILE A 200 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.60e+00 bond pdb=" CAL Y01 A 302 " pdb=" CAX Y01 A 302 " ideal model delta sigma weight residual 1.540 1.516 0.024 2.00e-02 2.50e+03 1.49e+00 ... (remaining 4049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 4924 1.08 - 2.17: 496 2.17 - 3.25: 86 3.25 - 4.34: 12 4.34 - 5.42: 16 Bond angle restraints: 5534 Sorted by residual: angle pdb=" N ARG A 79 " pdb=" CA ARG A 79 " pdb=" C ARG A 79 " ideal model delta sigma weight residual 108.74 105.16 3.58 1.38e+00 5.25e-01 6.75e+00 angle pdb=" N ARG B 79 " pdb=" CA ARG B 79 " pdb=" C ARG B 79 " ideal model delta sigma weight residual 108.74 105.16 3.58 1.38e+00 5.25e-01 6.74e+00 angle pdb=" N GLY A 117 " pdb=" CA GLY A 117 " pdb=" C GLY A 117 " ideal model delta sigma weight residual 113.18 118.60 -5.42 2.37e+00 1.78e-01 5.24e+00 angle pdb=" N GLY B 117 " pdb=" CA GLY B 117 " pdb=" C GLY B 117 " ideal model delta sigma weight residual 113.18 118.57 -5.39 2.37e+00 1.78e-01 5.18e+00 angle pdb=" N GLU B 32 " pdb=" CA GLU B 32 " pdb=" C GLU B 32 " ideal model delta sigma weight residual 109.81 114.60 -4.79 2.21e+00 2.05e-01 4.69e+00 ... (remaining 5529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 2360 17.21 - 34.41: 132 34.41 - 51.62: 22 51.62 - 68.82: 4 68.82 - 86.02: 2 Dihedral angle restraints: 2520 sinusoidal: 1100 harmonic: 1420 Sorted by residual: dihedral pdb=" CA HIS A 98 " pdb=" C HIS A 98 " pdb=" N ALA A 99 " pdb=" CA ALA A 99 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA HIS B 98 " pdb=" C HIS B 98 " pdb=" N ALA B 99 " pdb=" CA ALA B 99 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASP A 204 " pdb=" C ASP A 204 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " ideal model delta harmonic sigma weight residual 180.00 161.68 18.32 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 2517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 277 0.032 - 0.063: 231 0.063 - 0.095: 99 0.095 - 0.126: 31 0.126 - 0.158: 12 Chirality restraints: 650 Sorted by residual: chirality pdb=" CA LEU A 208 " pdb=" N LEU A 208 " pdb=" C LEU A 208 " pdb=" CB LEU A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CA LEU B 208 " pdb=" N LEU B 208 " pdb=" C LEU B 208 " pdb=" CB LEU B 208 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA THR B 93 " pdb=" N THR B 93 " pdb=" C THR B 93 " pdb=" CB THR B 93 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 647 not shown) Planarity restraints: 668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 173 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.68e+00 pdb=" C ILE A 173 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE A 173 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A 174 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 20 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C LEU B 20 " 0.045 2.00e-02 2.50e+03 pdb=" O LEU B 20 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL B 21 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 173 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C ILE B 173 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE B 173 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY B 174 " 0.015 2.00e-02 2.50e+03 ... (remaining 665 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.95: 1809 2.95 - 3.50: 4785 3.50 - 4.05: 7006 4.05 - 4.59: 10684 4.59 - 5.14: 14537 Nonbonded interactions: 38821 Sorted by model distance: nonbonded pdb=" O THR A 198 " pdb=" OG1 THR A 199 " model vdw 2.404 3.040 nonbonded pdb=" O THR B 198 " pdb=" OG1 THR B 199 " model vdw 2.404 3.040 nonbonded pdb=" OH TYR B 96 " pdb=" OG1 THR B 196 " model vdw 2.420 3.040 nonbonded pdb=" OH TYR A 96 " pdb=" OG1 THR A 196 " model vdw 2.421 3.040 nonbonded pdb=" OE2 GLU A 182 " pdb=" OH TYR A 220 " model vdw 2.423 3.040 ... (remaining 38816 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 302) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.670 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 4054 Z= 0.299 Angle : 0.749 5.423 5534 Z= 0.442 Chirality : 0.052 0.158 650 Planarity : 0.006 0.026 668 Dihedral : 11.299 86.025 1612 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.34), residues: 480 helix: -0.43 (0.23), residues: 396 sheet: None (None), residues: 0 loop : -1.24 (0.70), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 38 TYR 0.023 0.004 TYR A 85 PHE 0.019 0.002 PHE A 202 TRP 0.007 0.001 TRP A 78 HIS 0.001 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00715 ( 4054) covalent geometry : angle 0.74910 ( 5534) hydrogen bonds : bond 0.07682 ( 314) hydrogen bonds : angle 5.11725 ( 924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.140 Fit side-chains REVERT: A 44 ARG cc_start: 0.6659 (ttt90) cc_final: 0.6434 (ttt-90) REVERT: A 130 GLU cc_start: 0.7342 (tm-30) cc_final: 0.6543 (tm-30) REVERT: A 135 LEU cc_start: 0.7284 (tp) cc_final: 0.6593 (mp) REVERT: A 249 MET cc_start: 0.5337 (ttt) cc_final: 0.5109 (ttp) REVERT: B 44 ARG cc_start: 0.6659 (ttt90) cc_final: 0.6435 (ttt-90) REVERT: B 130 GLU cc_start: 0.7351 (tm-30) cc_final: 0.6552 (tm-30) REVERT: B 135 LEU cc_start: 0.7280 (tp) cc_final: 0.6592 (mp) REVERT: B 249 MET cc_start: 0.5342 (ttt) cc_final: 0.5115 (ttp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0846 time to fit residues: 6.7875 Evaluate side-chains 56 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN B 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.177890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.116446 restraints weight = 3844.171| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.41 r_work: 0.3129 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4054 Z= 0.130 Angle : 0.509 4.941 5534 Z= 0.275 Chirality : 0.039 0.155 650 Planarity : 0.003 0.016 668 Dihedral : 5.425 50.538 818 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.52 % Allowed : 5.15 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.50 (0.39), residues: 480 helix: 1.97 (0.26), residues: 392 sheet: None (None), residues: 0 loop : 0.41 (0.80), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 137 TYR 0.014 0.001 TYR A 85 PHE 0.012 0.001 PHE A 109 TRP 0.003 0.000 TRP A 184 HIS 0.001 0.000 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4054) covalent geometry : angle 0.50926 ( 5534) hydrogen bonds : bond 0.03704 ( 314) hydrogen bonds : angle 3.67486 ( 924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.146 Fit side-chains REVERT: A 135 LEU cc_start: 0.6994 (tp) cc_final: 0.6378 (mp) REVERT: B 135 LEU cc_start: 0.6988 (tp) cc_final: 0.6375 (mp) outliers start: 2 outliers final: 2 residues processed: 54 average time/residue: 0.0978 time to fit residues: 6.3454 Evaluate side-chains 46 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 5 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 41 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.177569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.117719 restraints weight = 3829.597| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.26 r_work: 0.3035 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4054 Z= 0.160 Angle : 0.510 5.089 5534 Z= 0.273 Chirality : 0.040 0.158 650 Planarity : 0.003 0.017 668 Dihedral : 5.460 49.307 818 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.55 % Allowed : 6.19 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.26 (0.40), residues: 480 helix: 2.42 (0.26), residues: 392 sheet: None (None), residues: 0 loop : 1.06 (0.84), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.012 0.001 TYR A 85 PHE 0.010 0.001 PHE A 109 TRP 0.001 0.000 TRP B 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 4054) covalent geometry : angle 0.50982 ( 5534) hydrogen bonds : bond 0.03804 ( 314) hydrogen bonds : angle 3.53425 ( 924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.177 Fit side-chains REVERT: A 135 LEU cc_start: 0.7077 (tp) cc_final: 0.6463 (mp) REVERT: B 135 LEU cc_start: 0.7071 (tp) cc_final: 0.6461 (mp) outliers start: 6 outliers final: 4 residues processed: 58 average time/residue: 0.0890 time to fit residues: 6.2801 Evaluate side-chains 48 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN B 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.177203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.117035 restraints weight = 3787.030| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.28 r_work: 0.3001 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4054 Z= 0.149 Angle : 0.488 5.087 5534 Z= 0.261 Chirality : 0.039 0.155 650 Planarity : 0.002 0.017 668 Dihedral : 5.405 47.466 818 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.03 % Allowed : 6.70 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.55 (0.40), residues: 480 helix: 2.60 (0.26), residues: 392 sheet: None (None), residues: 0 loop : 1.26 (0.88), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 137 TYR 0.010 0.001 TYR A 85 PHE 0.010 0.001 PHE A 109 TRP 0.003 0.001 TRP B 78 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 4054) covalent geometry : angle 0.48814 ( 5534) hydrogen bonds : bond 0.03596 ( 314) hydrogen bonds : angle 3.40670 ( 924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.158 Fit side-chains REVERT: A 135 LEU cc_start: 0.7085 (tp) cc_final: 0.6453 (mp) REVERT: B 135 LEU cc_start: 0.7077 (tp) cc_final: 0.6450 (mp) outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 0.1081 time to fit residues: 6.5150 Evaluate side-chains 48 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.178107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.118505 restraints weight = 3796.721| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.25 r_work: 0.2992 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4054 Z= 0.133 Angle : 0.474 5.090 5534 Z= 0.251 Chirality : 0.038 0.152 650 Planarity : 0.003 0.018 668 Dihedral : 5.330 45.468 818 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.06 % Allowed : 6.70 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.80 (0.40), residues: 480 helix: 2.82 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 1.16 (0.83), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 44 TYR 0.009 0.001 TYR A 85 PHE 0.010 0.001 PHE A 109 TRP 0.003 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4054) covalent geometry : angle 0.47409 ( 5534) hydrogen bonds : bond 0.03414 ( 314) hydrogen bonds : angle 3.32698 ( 924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.145 Fit side-chains REVERT: A 135 LEU cc_start: 0.7007 (tp) cc_final: 0.6451 (mp) REVERT: B 135 LEU cc_start: 0.7014 (tp) cc_final: 0.6458 (mp) outliers start: 8 outliers final: 4 residues processed: 57 average time/residue: 0.0913 time to fit residues: 6.3129 Evaluate side-chains 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.175695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114492 restraints weight = 3892.322| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.30 r_work: 0.2939 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4054 Z= 0.134 Angle : 0.480 5.108 5534 Z= 0.255 Chirality : 0.038 0.150 650 Planarity : 0.003 0.025 668 Dihedral : 5.259 43.278 818 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.03 % Allowed : 6.44 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.94 (0.39), residues: 480 helix: 2.95 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 1.02 (0.81), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 137 TYR 0.009 0.001 TYR A 113 PHE 0.009 0.001 PHE A 109 TRP 0.004 0.001 TRP B 78 HIS 0.001 0.000 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 4054) covalent geometry : angle 0.48005 ( 5534) hydrogen bonds : bond 0.03365 ( 314) hydrogen bonds : angle 3.25779 ( 924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.138 Fit side-chains REVERT: A 135 LEU cc_start: 0.6985 (tp) cc_final: 0.6408 (mp) REVERT: B 135 LEU cc_start: 0.6986 (tp) cc_final: 0.6412 (mp) outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 0.0894 time to fit residues: 5.4176 Evaluate side-chains 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.175908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114286 restraints weight = 3866.883| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.32 r_work: 0.2940 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4054 Z= 0.134 Angle : 0.478 5.108 5534 Z= 0.253 Chirality : 0.038 0.145 650 Planarity : 0.003 0.025 668 Dihedral : 5.158 38.862 818 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.55 % Allowed : 6.70 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.04 (0.39), residues: 480 helix: 3.04 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 0.97 (0.80), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 137 TYR 0.009 0.001 TYR B 113 PHE 0.009 0.001 PHE B 109 TRP 0.004 0.001 TRP B 78 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 4054) covalent geometry : angle 0.47768 ( 5534) hydrogen bonds : bond 0.03314 ( 314) hydrogen bonds : angle 3.23020 ( 924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.140 Fit side-chains REVERT: A 135 LEU cc_start: 0.6948 (tp) cc_final: 0.6377 (mp) REVERT: B 135 LEU cc_start: 0.6958 (tp) cc_final: 0.6396 (mp) outliers start: 6 outliers final: 6 residues processed: 52 average time/residue: 0.0933 time to fit residues: 5.8413 Evaluate side-chains 54 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.174565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112315 restraints weight = 3842.608| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.32 r_work: 0.2992 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4054 Z= 0.152 Angle : 0.494 5.168 5534 Z= 0.262 Chirality : 0.039 0.147 650 Planarity : 0.003 0.025 668 Dihedral : 5.182 38.432 818 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.55 % Allowed : 7.22 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.00 (0.39), residues: 480 helix: 3.01 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 0.97 (0.80), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 137 TYR 0.009 0.001 TYR B 113 PHE 0.009 0.001 PHE B 109 TRP 0.003 0.001 TRP B 78 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 4054) covalent geometry : angle 0.49382 ( 5534) hydrogen bonds : bond 0.03482 ( 314) hydrogen bonds : angle 3.28281 ( 924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.136 Fit side-chains REVERT: A 135 LEU cc_start: 0.6995 (tp) cc_final: 0.6442 (mp) REVERT: B 135 LEU cc_start: 0.6987 (tp) cc_final: 0.6437 (mp) outliers start: 6 outliers final: 6 residues processed: 53 average time/residue: 0.0946 time to fit residues: 6.0383 Evaluate side-chains 54 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.0070 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.181009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.118959 restraints weight = 3901.939| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.36 r_work: 0.3092 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4054 Z= 0.110 Angle : 0.487 11.739 5534 Z= 0.245 Chirality : 0.037 0.148 650 Planarity : 0.003 0.023 668 Dihedral : 4.919 37.307 818 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.03 % Allowed : 7.99 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.16 (0.39), residues: 480 helix: 3.14 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 0.89 (0.80), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 137 TYR 0.008 0.001 TYR B 113 PHE 0.009 0.001 PHE A 109 TRP 0.005 0.001 TRP A 184 HIS 0.000 0.000 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 4054) covalent geometry : angle 0.48669 ( 5534) hydrogen bonds : bond 0.03027 ( 314) hydrogen bonds : angle 3.13109 ( 924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.174 Fit side-chains REVERT: A 135 LEU cc_start: 0.6991 (tp) cc_final: 0.6400 (mp) REVERT: B 135 LEU cc_start: 0.6999 (tp) cc_final: 0.6408 (mp) outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 0.0983 time to fit residues: 5.9133 Evaluate side-chains 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.179723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.117508 restraints weight = 3831.640| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.34 r_work: 0.2993 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4054 Z= 0.124 Angle : 0.497 10.753 5534 Z= 0.252 Chirality : 0.038 0.146 650 Planarity : 0.003 0.023 668 Dihedral : 4.919 36.566 818 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.03 % Allowed : 8.51 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.17 (0.39), residues: 480 helix: 3.15 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 0.88 (0.80), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 137 TYR 0.009 0.001 TYR A 113 PHE 0.009 0.001 PHE B 109 TRP 0.004 0.001 TRP B 78 HIS 0.001 0.000 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 4054) covalent geometry : angle 0.49721 ( 5534) hydrogen bonds : bond 0.03163 ( 314) hydrogen bonds : angle 3.16320 ( 924) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.141 Fit side-chains REVERT: A 135 LEU cc_start: 0.6962 (tp) cc_final: 0.6379 (mp) REVERT: B 135 LEU cc_start: 0.6962 (tp) cc_final: 0.6382 (mp) outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 0.0952 time to fit residues: 5.7339 Evaluate side-chains 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 4 optimal weight: 0.0570 chunk 31 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.177549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.115606 restraints weight = 3855.454| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.31 r_work: 0.3084 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4054 Z= 0.119 Angle : 0.511 10.574 5534 Z= 0.252 Chirality : 0.037 0.146 650 Planarity : 0.003 0.022 668 Dihedral : 4.850 35.603 818 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.03 % Allowed : 8.51 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.23 (0.39), residues: 480 helix: 3.19 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 0.91 (0.80), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 137 TYR 0.009 0.001 TYR B 113 PHE 0.009 0.001 PHE B 109 TRP 0.004 0.001 TRP A 78 HIS 0.001 0.000 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4054) covalent geometry : angle 0.51129 ( 5534) hydrogen bonds : bond 0.03077 ( 314) hydrogen bonds : angle 3.13670 ( 924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1327.96 seconds wall clock time: 23 minutes 31.30 seconds (1411.30 seconds total)